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MixtureTree annotator: a program for automatic colorization and visual annotation of MixtureTree.

Chen SC, Ogata A - PLoS ONE (2015)

Bottom Line: In order to visualize the resulting output file, a modified version of FigTree is used.Certain popular methods, which lack good built-in visualization tools, for example, MEGA, Mesquite, PHY-FI, TreeView, treeGraph and Geneious, may give results with human errors due to either manually adding colors to each node or with other limitations, for example only using color based on a number, such as branch length, or by taxonomy.The MixtureTree Annotator is fast and easy-to-use, while still allowing the user full control over the coloring and annotating process.

View Article: PubMed Central - PubMed

Affiliation: Department of Mathematics, Idaho State University, Pocatello, Idaho, United States of America.

ABSTRACT
The MixtureTree Annotator, written in JAVA, allows the user to automatically color any phylogenetic tree in Newick format generated from any phylogeny reconstruction program and output the Nexus file. By providing the ability to automatically color the tree by sequence name, the MixtureTree Annotator provides a unique advantage over any other programs which perform a similar function. In addition, the MixtureTree Annotator is the only package that can efficiently annotate the output produced by MixtureTree with mutation information and coalescent time information. In order to visualize the resulting output file, a modified version of FigTree is used. Certain popular methods, which lack good built-in visualization tools, for example, MEGA, Mesquite, PHY-FI, TreeView, treeGraph and Geneious, may give results with human errors due to either manually adding colors to each node or with other limitations, for example only using color based on a number, such as branch length, or by taxonomy. In addition to allowing the user to automatically color any given Newick tree by sequence name, the MixtureTree Annotator is the only method that allows the user to automatically annotate the resulting tree created by the MixtureTree program. The MixtureTree Annotator is fast and easy-to-use, while still allowing the user full control over the coloring and annotating process.

No MeSH data available.


Related in: MedlinePlus

Default Coloring Page of MixtureTree Annotator.
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pone.0118893.g002: Default Coloring Page of MixtureTree Annotator.

Mentions: Colorization in Newick trees is important because it enables the user to quickly and accurately visualize clusters of DNA sequences, especially when the sample size is large. A typical coloring screen is shown in Fig 2, in which the different lineages are listed on the left and the color picker is on the right. Based on user preference, the YRI population group could be colored red and the Eu_Am population group colored in blue. A Newick tree normally consists of a single, solid black color. However, as shown in Fig 3, the benefits of tree colorization are clear. One immediately notices two large distinct clusters, namely the distinct Eu_Am and YRI groups. The advantage of this package is that by clicking on the color picker, the user can easily assign a color to each group or sequence.


MixtureTree annotator: a program for automatic colorization and visual annotation of MixtureTree.

Chen SC, Ogata A - PLoS ONE (2015)

Default Coloring Page of MixtureTree Annotator.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4380466&req=5

pone.0118893.g002: Default Coloring Page of MixtureTree Annotator.
Mentions: Colorization in Newick trees is important because it enables the user to quickly and accurately visualize clusters of DNA sequences, especially when the sample size is large. A typical coloring screen is shown in Fig 2, in which the different lineages are listed on the left and the color picker is on the right. Based on user preference, the YRI population group could be colored red and the Eu_Am population group colored in blue. A Newick tree normally consists of a single, solid black color. However, as shown in Fig 3, the benefits of tree colorization are clear. One immediately notices two large distinct clusters, namely the distinct Eu_Am and YRI groups. The advantage of this package is that by clicking on the color picker, the user can easily assign a color to each group or sequence.

Bottom Line: In order to visualize the resulting output file, a modified version of FigTree is used.Certain popular methods, which lack good built-in visualization tools, for example, MEGA, Mesquite, PHY-FI, TreeView, treeGraph and Geneious, may give results with human errors due to either manually adding colors to each node or with other limitations, for example only using color based on a number, such as branch length, or by taxonomy.The MixtureTree Annotator is fast and easy-to-use, while still allowing the user full control over the coloring and annotating process.

View Article: PubMed Central - PubMed

Affiliation: Department of Mathematics, Idaho State University, Pocatello, Idaho, United States of America.

ABSTRACT
The MixtureTree Annotator, written in JAVA, allows the user to automatically color any phylogenetic tree in Newick format generated from any phylogeny reconstruction program and output the Nexus file. By providing the ability to automatically color the tree by sequence name, the MixtureTree Annotator provides a unique advantage over any other programs which perform a similar function. In addition, the MixtureTree Annotator is the only package that can efficiently annotate the output produced by MixtureTree with mutation information and coalescent time information. In order to visualize the resulting output file, a modified version of FigTree is used. Certain popular methods, which lack good built-in visualization tools, for example, MEGA, Mesquite, PHY-FI, TreeView, treeGraph and Geneious, may give results with human errors due to either manually adding colors to each node or with other limitations, for example only using color based on a number, such as branch length, or by taxonomy. In addition to allowing the user to automatically color any given Newick tree by sequence name, the MixtureTree Annotator is the only method that allows the user to automatically annotate the resulting tree created by the MixtureTree program. The MixtureTree Annotator is fast and easy-to-use, while still allowing the user full control over the coloring and annotating process.

No MeSH data available.


Related in: MedlinePlus